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Vallejo J, Saigusa R, Gulati R, Armstrong Suthahar SS, Suryawanshi V, Alimadadi A, Durant CP, Ghosheh Y, Roy P, Ehinger E, Pattarabanjird T, Hanna DB, Landay AL, Tracy RP, Lazar JM, Mack WJ, Weber KM, Adimora AA, Hodis HN, Tien PC, Ofotokun I, Heath SL, Shemesh A, McNamara CA, Lanier LL, Hedrick CC, Kaplan RC, Ley K. Combined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells. BMC Biol 2022; 20:193. [PMID: 36045343 PMCID: PMC9434837 DOI: 10.1186/s12915-022-01382-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/01/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single-cell (sc)RNA sequencing (scRNA-seq) in PBMCs. RESULTS Among 31 participants in the Women's Interagency HIV Study (WIHS), we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs (tool for visualizing high-dimensional data) and Louvain clustering, we identified 50 subsets among CD4+ T, CD8+ T, B, NK cells, and monocytes. This resolution was superior to flow cytometry, mass cytometry, or scRNA-seq without antibodies. Combined protein and transcript scRNA-seq allowed for the assessment of disease-related changes in transcriptomes and cell type proportions. As a proof-of-concept, we showed such differences between healthy and matched individuals living with HIV with and without cardiovascular disease. CONCLUSIONS In conclusion, combined protein and transcript scRNA sequencing is a suitable and powerful method for clinical investigations using PBMCs.
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Affiliation(s)
- Jenifer Vallejo
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Ryosuke Saigusa
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Rishab Gulati
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | | | | | - Ahmad Alimadadi
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | | | - Yanal Ghosheh
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Payel Roy
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Erik Ehinger
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Tanyaporn Pattarabanjird
- Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Jason M Lazar
- Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Wendy J Mack
- Department of Medicine and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Kathleen M Weber
- Cook County Health/Hektoen Institute of Medicine, Chicago, IL, USA
| | - Adaora A Adimora
- Department of Medicine, University of North Carolina School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Howard N Hodis
- Department of Medicine and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Atherosclerosis Research Unit, University of Southern California, Los Angeles, CA, USA
| | - Phyllis C Tien
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Igho Ofotokun
- Department of Medicine, Infectious Disease Division and Grady Health Care System, Emory University School of Medicine, Atlanta, GA, USA
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avishai Shemesh
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Coleen A McNamara
- Carter Immunology Center, Cardiovascular Division, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Lewis L Lanier
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Catherine C Hedrick
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - Klaus Ley
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA.
- Immunology Center of Georgia, Augusta University, Augusta, GA, USA.
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